Accelerating Smith-Waterman Alignment of Long DNA Sequences with OpenCL on FPGA View Full Text


Ontology type: schema:Chapter     


Chapter Info

DATE

2017

AUTHORS

Enzo Rucci , Carlos Garcia , Guillermo Botella , Armando De Giusti , Marcelo Naiouf , Manuel Prieto-Matias

ABSTRACT

With the greater importance of parallel architectures such as GPUs or Xeon Phi accelerators, the scientific community has developed efficient solutions in the bioinformatics field. In this context, FPGAs begin to stand out as high performance devices with moderate power consumption. This paper presents and evaluates a parallel strategy of the well-known Smith-Waterman algorithm using OpenCL on Intel/Altera’s FPGA for long DNA sequences. We efficiently exploit data and pipeline parallelism on a Intel/Altera Stratix V FPGA reaching upto 114 GCUPS in less than 25 watt power requirements. More... »

PAGES

500-511

Book

TITLE

Bioinformatics and Biomedical Engineering

ISBN

978-3-319-56153-0
978-3-319-56154-7

Identifiers

URI

http://scigraph.springernature.com/pub.10.1007/978-3-319-56154-7_45

DOI

http://dx.doi.org/10.1007/978-3-319-56154-7_45

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1084754024


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